[gmx-users] C-terminal amide capping

[Justin A. Lemkul]

ANINDITA GAYEN wrote:
> 
> Dear all,
>             I do simulate DMPC+peptide+water+ions system, using OPLS-AA 
> force field.
> My peptide has N-terminus: NH3+ & C-terminus: COO- groups. I want to 
> convert it to
> N-terminus: NH2, C-terminus: CONH2. The N-terminal capping is easily 
> done using "pdb2gmx -ter " command, but C-terminal amide capping option 
> is not incorporated.

What do you mean, "not incorporated"?  You should be able to do it exactly as 
you did with the N-terminus.  You must include the -NH2 in your structure file, 
and then process with pdb2gmx -ter.

-Justin

> Can anyone please suggests me how i can achive this?
> Thanks in advance.
> 
> Ms. Anindita Gayen
>  > C/O Dr. Chaitali Mukhopadhyay
> Senior Research Fellow
> Department of Chemistry
> University of Calcutta
> 92, A. P. C. Road
> Kolkata-700 009
> India
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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